Petr Danecek

Just to link it to a related issue in htslib: https://github.com/samtools/htslib/issues/1424

I just received the same error, apparently this can still happen https://cirrus-ci.com/task/6336215039868928?logs=test#L6624 ``` test_naive_concat: /tmp/cirrus-ci-build/bcftools concat --naive /tmp/jSUwzfxxPq/naive_concat.0.vcf.gz /tmp/jSUwzfxxPq/naive_concat.1.vcf.gz /tmp/jSUwzfxxPq/naive_concat.2.vcf.gz /tmp/jSUwzfxxPq/naive_concat.3.vcf.gz /tmp/jSUwzfxxPq/naive_concat.4.vcf.gz /tmp/jSUwzfxxPq/naive_concat.5.vcf.gz /tmp/jSUwzfxxPq/naive_concat.6.vcf.gz /tmp/jSUwzfxxPq/naive_concat.7.vcf.gz /tmp/jSUwzfxxPq/naive_concat.8.vcf.gz /tmp/jSUwzfxxPq/naive_concat.9.vcf.gz | /tmp/cirrus-ci-build/bcftools view...

Unfortunately not. It is one of the desired features, but it was not implemented yet. See also https://github.com/samtools/bcftools/issues/1843

I am unable to reproduce the problem. Can you show the header (definitions of all tags with unexpected outcome), plus one input line in all three VCFs?

Hi, in principle the request is sound, however for this specific case I see two problems. First, DP is a tag reserved by the VCF specification as Number=1, so it...

The `norm` command treats `*` as if it was a normal allele. After splitting such records don't carry much information, so I guess normally it is safe to remove them,...

The only working solution for now is to fix the header to include all the missing tags (`bcftools reheader`) or drop the undefined tags (`bcftools annotate -x`). This is because...

A possible enhancement would be to sort VCFs natively, without the need for BCF conversion. This was planned but never high enough on the priority list. Marking it as an...

The differences in depth are impossible to explain just from looking at screenshots. You'd need to look at all reads, check their flags etc. The genotypes can be determined by...

Just noting here that this was also requested in https://github.com/samtools/bcftools/issues/1670, and also see the comment https://github.com/samtools/bcftools/issues/1670#issuecomment-1061865432